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This study brings together plot-scale growing season fluxes of carbon dioxide (CO2) and methane (CH4) from six Canadian peatlands restored by the moss layer transfer technique (MLTT) and compares them with fluxes from adjacent unrestored and natural peatlands to determine: 1) if CO2 and CH4 fluxes return to natural-site levels and 2) whether the ecohydrological controls (e.g. water table, plant cover) on these fluxes are similar between treatments. We also examine differences between eastern (humid/maritime climate) and western (subhumid climate) Canadian plots, and between restoration of former horticultural peat extraction sites and oil industry well-pads. Our results indicate that restored site fluxes of CO2 and CH4 are not significantly different between eastern and western Canada or between a restored well-pad and restored horticultural peat extraction sites. Restoration resulted in gross primary production rates similar to those at natural plots and significantly greater than those at unrestored plots. Ecosystem respiration was not significantly different at restored and unrestored plots, and was lower at both than at natural plots. Methane emission was significantly greater at restored plots than at unrestored plots, but remained significantly lower on average than at natural plots. Water table was a significant control on CH4 flux across restored and natural plots. Vascular plant cover was significantly related to CO2 uptake (gross photosynthesis) at restored and unrestored plots, but not at natural plots, while higher moss cover resulted in significantly greater net uptake of CO2 at natural plots but not at restored and unrestored plots. Overall, MLTT restoration greatly alters CO2 and CH4 dynamics compared to unrestored areas but fluxes remain, on average, significantly different from those in natural peatlands, in both the magnitude of mean growing season fluxes and controls on variation in these fluxes among plots. Peatland restoration by MLTT results in reduced CO2 emissions and higher CH4 emissions; however, more year-round measurements in more restored peatlands over longer periods post-restoration are needed to improve greenhouse gas emission estimates for restored Canadian peatlands.